| Field | Description |
|---|---|
| SampleID | Name of the sample |
| TrimReads | Total number of reads after quality filtering |
| MeanReadLen | Average read length after quality filtering |
| Contigs | Number of contigs of the draft genome (>200bp) |
| GenomeLength | Length (bp) of the draft genome |
| LargestContig | Length (bp) of the largest contig in the genome |
| N50 | Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly |
| GC-Content | GC content (%) of the draft genome |
| Depth | Number of times each nucleotide position in the draft genome has a read that aligns to that position |
| SampleID | TrimReads | MeanReadLen | Contigs | GenomeLength | LargestContig | N50 | GC-Content | Depth |
|---|---|---|---|---|---|---|---|---|
| ID084I | 355637 | 132 | 62 | 5074296 | 548642 | 225746 | 51.66 | 9X |
| ORTHO013EII | 345294 | 133 | 2785 | 8669942 | 55924 | 5621 | 55.41 | 5X |
| ORTHO039E | 433286 | 133 | 102 | 5004643 | 337885 | 124175 | 55.00 | 11X |
Average number of reads per sample = 378072
Average read length per sample = 133 bp
Average number of contigs per sample = 983
Average genome length per sample = 6249627 bp
Average largest contig length per sample = 314150 bp
Average N50 per sample = 118514 bp
Average GC content per sample = 54.023%
Average sequencing depth = 8.333X
| Field | Description |
|---|---|
| GenomePosition | Position in the genome where SNP is found |
| Type | Nature of the SNP identified (Only ‘True’ SNPs are shown by default) |
| ReferenceAllele | Allele found in the reference genome |
| AlternateAllele | Allele found in the genome of interest forming the SNP |
| Consequence | Amino acid alterations caused by the SNP |
| AffectedGene | The tartget gene affected by the SNP |
| Product | The outcome from the presence of the SNP |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 1619514 | snp | A | C | missense_variant c.1014T>G p.His338Gln | NA | phage resistance protein |
| 1680903 | snp | T | C | missense_variant c.406T>C p.Trp136Arg | NA | multidrug resistance outer membrane protein MdtQ |
| 1681054 | snp | G | A | missense_variant c.557G>A p.Ser186Asn | NA | multidrug resistance outer membrane protein MdtQ |
| 2153125 | snp | T | C | missense_variant c.44T>C p.Ile15Thr | NA | putative copper resistance protein CopD |
| 2473709 | snp | G | A | missense_variant c.5G>A p.Ser2Asn | NA | tellurite resistance protein TehA |
| 2473825 | snp | G | A | missense_variant c.121G>A p.Gly41Ser | NA | tellurite resistance protein TehA |
| 2537962 | snp | C | T | missense_variant c.371C>T p.Ala124Val | NA | methyl viologen resistance protein SmvA |
| 2538486 | snp | T | G | missense_variant c.895T>G p.Leu299Val | NA | methyl viologen resistance protein SmvA |
| 2745862 | snp | A | T | missense_variant c.74A>T p.Gln25Leu | NA | fusaric acid resistance protein |
| 2746092 | snp | G | A | missense_variant c.304G>A p.Val102Met | NA | fusaric acid resistance protein |
| 2747688 | snp | G | A | missense_variant c.1900G>A p.Ala634Thr | NA | fusaric acid resistance protein |
| 2747736 | snp | A | G | missense_variant c.1948A>G p.Ile650Val | NA | fusaric acid resistance protein |
| 3068212 | snp | C | T | missense_variant c.284G>A p.Arg95Gln | NA | arsenic resistance operon repressor |
| 3068294 | snp | G | A | missense_variant c.202C>T p.His68Tyr | NA | arsenic resistance operon repressor |
| 3068389 | snp | G | A | missense_variant c.107C>T p.Ala36Val | NA | arsenic resistance operon repressor |
| 3068804 | snp | A | G | missense_variant c.224A>G p.Asp75Gly | NA | arsenical resistance protein ArsH |
| 3069242 | snp | A | T | missense_variant c.662A>T p.Gln221Leu | NA | arsenical resistance protein ArsH |
| 3839989 | snp | A | T | missense_variant c.539A>T p.Glu180Val | NA | oxidative-stress-resistance chaperone |
| 4708330 | snp | G | A | missense_variant c.646G>A p.Asp216Asn | NA | multidrug resistance efflux RND protein MdtN |
| 4708574 | snp | A | T | missense_variant c.890A>T p.Gln297Leu | NA | multidrug resistance efflux RND protein MdtN |
| 4709233 | snp | C | T | missense_variant c.518C>T p.Thr173Ile | NA | multidrug resistance efflux RND protein MdtO |
| 4709280 | snp | G | A | missense_variant c.565G>A p.Ala189Thr | NA | multidrug resistance efflux RND protein MdtO |
| 4709431 | snp | T | C | missense_variant c.716T>C p.Val239Ala | NA | multidrug resistance efflux RND protein MdtO |
| 4709685 | snp | A | G | missense_variant c.970A>G p.Asn324Asp | NA | multidrug resistance efflux RND protein MdtO |
| 4710312 | snp | A | G | missense_variant c.1597A>G p.Met533Val | NA | multidrug resistance efflux RND protein MdtO |
| 4710422 | snp | A | G | missense_variant c.1707A>G p.Ile569Met | NA | multidrug resistance efflux RND protein MdtO |
| 4710477 | snp | A | G | missense_variant c.1762A>G p.Thr588Ala | NA | multidrug resistance efflux RND protein MdtO |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 4579070 | snp | G | C | missense_variant c.639C>G p.Ile213Met | NA | tellurium resistance protein TerX |
| 4579107 | snp | A | T | missense_variant c.602T>A p.Val201Glu | NA | tellurium resistance protein TerX |
| 4579147 | snp | G | C | missense_variant c.562C>G p.Pro188Ala | NA | tellurium resistance protein TerX |
| 4579656 | snp | A | T | missense_variant c.53T>A p.Phe18Tyr | NA | tellurium resistance protein TerX |
| 4579877 | snp | T | C | missense_variant c.493A>G p.Thr165Ala | NA | tellerium resistance protein TerY |
| 4579973 | snp | T | C | missense_variant c.397A>G p.Thr133Ala | NA | tellerium resistance protein TerY |
| 4590524 | snp | A | G | missense_variant c.508A>G p.Thr170Ala | NA | tellurium resistance protein TerA |
| 4590567 | snp | A | C | missense_variant c.551A>C p.Lys184Thr | NA | tellurium resistance protein TerA |
| 4590680 | snp | A | G | missense_variant c.664A>G p.Ser222Gly | NA | tellurium resistance protein TerA |
| 4590696 | snp | G | C | missense_variant c.680G>C p.Gly227Ala | NA | tellurium resistance protein TerA |
| 4590800 | snp | G | A | missense_variant c.784G>A p.Asp262Asn | NA | tellurium resistance protein TerA |
| 4592008 | snp | G | A | missense_variant c.334G>A p.Val112Ile | NA | tellurium resistance protein TerC |
| 4592146 | snp | A | G | missense_variant c.472A>G p.Asn158Asp | NA | tellurium resistance protein TerC |
| 4592642 | snp | C | G | missense_variant c.968C>G p.Ala323Gly | NA | tellurium resistance protein TerC |
| 4592686 | snp | G | A | missense_variant c.1012G>A p.Glu338Lys | NA | tellurium resistance protein TerC |
| 4592694 | snp | T | A | missense_variant c.1020T>A p.Asp340Glu | NA | tellurium resistance protein TerC |
| 4592808 | snp | A | G | missense_variant c.46A>G p.Thr16Ala | NA | tellurium resistance protein TerD |
| 4592967 | snp | G | T | missense_variant c.205G>T p.Ala69Ser | NA | tellurium resistance protein TerD |
| 4593470 | snp | G | A | missense_variant c.64G>A p.Val22Ile | NA | chemical-damaging agent resistance protein C |
| 4593519 | snp | G | C | missense_variant c.113G>C p.Gly38Ala | NA | chemical-damaging agent resistance protein C |
| 4593745 | snp | A | T | missense_variant c.339A>T p.Glu113Asp | NA | chemical-damaging agent resistance protein C |
| 5028187 | snp | C | G | missense_variant c.391C>G p.Leu131Val | NA | chloramphenical resistance permease RarD |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 2638763 | snp | A | T | missense_variant c.382A>T p.Thr128Ser | NA | multiple antibiotic resistance transcriptional regulator MarR |
| 2638803 | snp | G | A | missense_variant c.422G>A p.Arg141Lys | NA | multiple antibiotic resistance transcriptional regulator MarR |
| 2638892 | snp | A | G | missense_variant c.58A>G p.Asn20Asp | NA | multiple antibiotic resistance transcriptional regulator MarA |
| 4579070 | snp | G | C | missense_variant c.639C>G p.Ile213Met | NA | tellurium resistance protein TerX |
| 4579107 | snp | A | T | missense_variant c.602T>A p.Val201Glu | NA | tellurium resistance protein TerX |
| 4579147 | snp | G | C | missense_variant c.562C>G p.Pro188Ala | NA | tellurium resistance protein TerX |
| 4579656 | snp | A | T | missense_variant c.53T>A p.Phe18Tyr | NA | tellurium resistance protein TerX |
| 4579877 | snp | T | C | missense_variant c.493A>G p.Thr165Ala | NA | tellerium resistance protein TerY |
| 4579973 | snp | T | C | missense_variant c.397A>G p.Thr133Ala | NA | tellerium resistance protein TerY |
| 4582643 | snp | A | G | missense_variant c.224T>C p.Ile75Thr | NA | tellurium resistance protein TerW |
| 4582708 | snp | A | C | missense_variant c.159T>G p.Asp53Glu | NA | tellurium resistance protein TerW |
| 4582779 | snp | C | T | missense_variant c.88G>A p.Ala30Thr | NA | tellurium resistance protein TerW |
| 4590375 | snp | A | G | missense_variant c.359A>G p.Asn120Ser | NA | tellurium resistance protein TerA |
| 4590524 | snp | A | G | missense_variant c.508A>G p.Thr170Ala | NA | tellurium resistance protein TerA |
| 4590567 | snp | A | C | missense_variant c.551A>C p.Lys184Thr | NA | tellurium resistance protein TerA |
| 4590680 | snp | A | G | missense_variant c.664A>G p.Ser222Gly | NA | tellurium resistance protein TerA |
| 4590696 | snp | G | C | missense_variant c.680G>C p.Gly227Ala | NA | tellurium resistance protein TerA |
| 4592008 | snp | G | A | missense_variant c.334G>A p.Val112Ile | NA | tellurium resistance protein TerC |
| 4592146 | snp | A | G | missense_variant c.472A>G p.Asn158Asp | NA | tellurium resistance protein TerC |
| 4592686 | snp | G | A | missense_variant c.1012G>A p.Glu338Lys | NA | tellurium resistance protein TerC |
| 4592694 | snp | T | A | missense_variant c.1020T>A p.Asp340Glu | NA | tellurium resistance protein TerC |
| 4592808 | snp | A | G | missense_variant c.46A>G p.Thr16Ala | NA | tellurium resistance protein TerD |
| 4593745 | snp | A | T | missense_variant c.339A>T p.Glu113Asp | NA | chemical-damaging agent resistance protein C |
| 5028013 | snp | A | G | missense_variant c.217A>G p.Ile73Val | NA | chloramphenical resistance permease RarD |
| 5028139 | snp | G | T | missense_variant c.343G>T p.Val115Leu | NA | chloramphenical resistance permease RarD |
| 5028187 | snp | C | G | missense_variant c.391C>G p.Leu131Val | NA | chloramphenical resistance permease RarD |
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Gaps | Gaps in subject (genome) and query (antibiotic resistance gene) |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
| Resistance | Antibiotic that the gene confers resistance to |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00041 | 3482 | 4081 | aac(6’)-Ib-cr_1 | 0/0 | 100.0 | 100.0 | DQ303918 | aac(6’)-Ib-cr | Ciprofloxacin |
| contig00041 | 1301 | 2146 | aadA16_1 | 0/0 | 100.0 | 99.6 | EU675686 | aadA16 | Streptomycin |
| contig00041 | 2933 | 3425 | ARR-3_4 | 0/0 | 90.8 | 99.2 | FM207631 | ARR-3 | |
| contig00017 | 99900 | 101045 | blaCMY-97_1 | 0/0 | 100.0 | 99.8 | KC007363 | blaCMY-97 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefotaxime, Cefoxitin, Ceftazidime, Piperacillin, Piperacillin+Tazobactam, Ticarcillin, Ticarcillin+Clavulanic_acid |
| contig00035 | 3701 | 4576 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00035 | 19 | 879 | blaTEM-1B_1 | 0/0 | 100.0 | 100.0 | AY458016 | blaTEM-1B | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig00041 | 2327 | 2800 | dfrA27_1 | 0/0 | 100.0 | 100.0 | FJ459817 | dfrA27 | Trimethoprim |
| contig00046 | 192 | 836 | qnrB6_2 | 0/0 | 100.0 | 100.0 | EF523819 | qnrB6 | Ciprofloxacin |
| contig00041 | 4 | 870 | sul1_5 | 0/0 | 100.0 | 99.9 | EU780013 | sul1 | Sulfamethoxazole |
| contig00037 | 2675 | 3490 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00035 | 7810 | 8994 | tet(D)_1 | 0/0 | 100.0 | 99.9 | AF467077 | tet(D) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00041 | 3482 | 4081 | AAC(6’)-Ib-cr | 0/0 | 100 | 100.0 | DQ303918:0-600 | AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously | aminoglycoside, fluoroquinolone |
| contig00041 | 1301 | 2146 | aadA16 | 0/0 | 100 | 99.6 | EU675686:3196-4042 | aadA16 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in E. coli V. cholerae and K. pneumoniae | aminoglycoside |
| contig00041 | 2933 | 3385 | arr-3 | 0/0 | 100 | 100.0 | EU675686:1956-2409 | arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis | rifamycin |
| contig00017 | 99900 | 101045 | CMY-65 | 0/0 | 100 | 99.6 | JF780936:63-1209 | CMY-65 is a beta-lactamase. From the Lahey list of CMY beta-lactamases. | cephamycin |
| contig00035 | 3701 | 4576 | CTX-M-15 | 0/0 | 100 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig00041 | 2327 | 2800 | dfrA27 | 0/0 | 100 | 100.0 | KP076293.1:2347-2821 | A dihydrofolate reductase and trimethoprim resistance gene from non-O1 non-O139 Vibrio cholerae | diaminopyrimidine |
| contig00002 | 419944 | 420357 | H-NS | 0/0 | 100 | 90.3 | BA000007.3:1738104-1737690 | H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. | cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline |
| contig00046 | 156 | 836 | QnrB17 | 0/0 | 100 | 99.8 | AM919398:0-681 | QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii | fluoroquinolone |
| contig00041 | 4 | 843 | sul1 | 0/0 | 100 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00037 | 2675 | 3490 | sul2 | 0/0 | 100 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00035 | 19 | 879 | TEM-1 | 0/0 | 100 | 99.9 | AL513383:161910-162771 | TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. | cephalosporin, monobactam, penam, penem |
| contig00035 | 7810 | 8994 | tet(D) | 0/0 | 100 | 99.9 | AF467077.1:163-1348 | TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00041 | 1301 | 2146 | (AGly)aadA16 | 0/0 | 100 | 99.6 | EU675686:3197-4042 | (AGly)aadA16 | NA |
| contig00017 | 99900 | 101045 | (Bla)blaCMY-66 | 0/0 | 100 | 99.4 | JN714478:1035-2180 | (Bla)blaCMY-66 | NA |
| contig00035 | 3701 | 4576 | (Bla)blaCTX-M-15 | 0/0 | 100 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig00035 | 19 | 879 | (Bla)blaTEM-105 | 0/0 | 100 | 99.9 | AF516720:215-1075 | (Bla)blaTEM-105 | NA |
| contig00046 | 156 | 836 | (Flq)qnrB17 | 0/0 | 100 | 99.8 | AM919398:1-681 | (Flq)qnrB17 | NA |
| contig00041 | 2933 | 3385 | (Rif)arr3 | 0/0 | 100 | 100.0 | JF806499:1353-1805 | (Rif)arr3 | NA |
| contig00041 | 4 | 843 | (Sul)sul1 | 0/0 | 100 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig00037 | 2675 | 3490 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00035 | 7810 | 8994 | (Tet)tetD | 0/0 | 100 | 99.9 | AB089602:1521-2705 | (Tet)tetD | NA |
| contig00041 | 2327 | 2800 | (Tmt)dfrA27 | 0/0 | 100 | 100.0 | EU675686:2543-3016 | (Tmt)dfrA27 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00041 | 3482 | 4036 | aac(6’)-Ib-D181Y | 0/0 | 100 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00041 | 1301 | 2146 | aadA16 | 0/0 | 100 | 100.0 | NG_047339.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA16 | STREPTOMYCIN |
| contig00041 | 2933 | 3385 | arr-3 | 0/0 | 100 | 100.0 | NG_048581.1 | NAD(+)–rifampin ADP-ribosyltransferase Arr-3 | RIFAMYCIN |
| contig00017 | 99900 | 101045 | blaCMY-97 | 0/0 | 100 | 99.8 | NG_048894.1 | class C beta-lactamase CMY-97 | CEPHALOSPORIN |
| contig00035 | 3701 | 4576 | blaCTX-M-15 | 0/0 | 100 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00035 | 19 | 879 | blaTEM-1 | 0/0 | 100 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00041 | 2327 | 2800 | dfrA27 | 0/0 | 100 | 100.0 | NG_047723.1 | trimethoprim-resistant dihydrofolate reductase DfrA27 | TRIMETHOPRIM |
| contig00046 | 192 | 836 | qnrB6 | 0/0 | 100 | 99.8 | NG_050523.1 | quinolone resistance pentapeptide repeat protein QnrB6 | QUINOLONE |
| contig00041 | 4 | 843 | sul1 | 0/0 | 100 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig00037 | 2675 | 3490 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00035 | 7810 | 8994 | tet(D) | 0/0 | 100 | 99.8 | NG_048184.1 | tetracycline efflux MFS transporter Tet(D) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00041 | 3482 | 4036 | aac(6’)-Ib-D181Y | 0/0 | 100 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00041 | 1301 | 2146 | aadA16 | 0/0 | 100 | 100.0 | NG_047339.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA16 | STREPTOMYCIN |
| contig00041 | 2933 | 3385 | arr-3 | 0/0 | 100 | 100.0 | NG_048581.1 | NAD(+)–rifampin ADP-ribosyltransferase Arr-3 | RIFAMYCIN |
| contig00017 | 99900 | 101045 | blaCMY-97 | 0/0 | 100 | 99.8 | NG_048894.1 | class C beta-lactamase CMY-97 | CEPHALOSPORIN |
| contig00035 | 3701 | 4576 | blaCTX-M-15 | 0/0 | 100 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00035 | 19 | 879 | blaTEM-1 | 0/0 | 100 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00041 | 2327 | 2800 | dfrA27 | 0/0 | 100 | 100.0 | NG_047723.1 | trimethoprim-resistant dihydrofolate reductase DfrA27 | TRIMETHOPRIM |
| contig00046 | 192 | 836 | qnrB6 | 0/0 | 100 | 99.8 | NG_050523.1 | quinolone resistance pentapeptide repeat protein QnrB6 | QUINOLONE |
| contig00041 | 4 | 843 | sul1 | 0/0 | 100 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig00037 | 2675 | 3490 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00035 | 7810 | 8994 | tet(D) | 0/0 | 100 | 99.8 | NG_048184.1 | tetracycline efflux MFS transporter Tet(D) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00899 | 1696 | 2556 | aac(3)-IIa_1 | 0/0 | 100.0 | 99.8 | X51534 | aac(3)-IIa | Gentamicin, Tobramycin |
| contig01080 | 1539 | 2138 | aac(6’)-Ib-cr_1 | 0/0 | 100.0 | 100.0 | DQ303918 | aac(6’)-Ib-cr | Ciprofloxacin |
| contig01058 | 1408 | 2211 | aph(3’’)-Ib_5 | 0/0 | 100.0 | 100.0 | AF321551 | aph(3’’)-Ib | Streptomycin |
| contig01058 | 572 | 1408 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00346 | 2798 | 3936 | blaACT-16_1 | 0/0 | 99.9 | 99.5 | AB737978 | blaACT-16 | |
| contig00047 | 3060 | 4205 | blaACT-6_1 | 0/0 | 100.0 | 91.9 | FJ237366 | blaACT-6 | |
| contig00230 | 2634 | 3509 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig01080 | 578 | 1408 | blaOXA-1_1 | 0/0 | 100.0 | 100.0 | HQ170510 | blaOXA-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig00012 | 2816 | 3676 | blaTEM-1A_1 | 0/0 | 100.0 | 100.0 | HM749966 | blaTEM-1A | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig01588 | 89 | 730 | catA2_1 | 0/0 | 100.0 | 96.1 | X53796 | catA2 | Chloramphenicol |
| contig02077 | 445 | 927 | dfrA14_5 | 0/0 | 100.0 | 99.6 | DQ388123 | dfrA14 | Trimethoprim |
| contig00515 | 2666 | 3139 | dfrA15_2 | 0/0 | 100.0 | 100.0 | AF221900 | dfrA15 | Trimethoprim |
| contig01687 | 1 | 642 | qnrB1_1 | 0/0 | 99.5 | 100.0 | DQ351241 | qnrB1 | Ciprofloxacin |
| contig00515 | 429 | 1295 | sul1_5 | 0/0 | 100.0 | 99.8 | EU780013 | sul1 | Sulfamethoxazole |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00899 | 1696 | 2556 | AAC(3)-IIe | 0/0 | 100.0 | 99.5 | EU022315.1:0-861 | AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig01080 | 1539 | 2138 | AAC(6’)-Ib-cr | 0/0 | 100.0 | 100.0 | DQ303918:0-600 | AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously | aminoglycoside, fluoroquinolone |
| contig00346 | 2791 | 3936 | ACT-25 | 0/0 | 100.0 | 99.3 | KJ207208:539-1685 | ACT-25 is a beta-lactamase. From the Lahey list of ACT beta-lactamases. | carbapenem, cephalosporin, cephamycin, penam |
| contig00047 | 3060 | 4205 | ACT-6 | 0/0 | 100.0 | 91.9 | FJ237366:40-1186 | ACT-6 is a beta-lactamase found in Klebsiella pneumoniae | carbapenem, cephalosporin, cephamycin, penam |
| contig01058 | 1408 | 2211 | APH(3’’)-Ib | 0/0 | 100.0 | 99.8 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig01058 | 572 | 1408 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig01588 | 89 | 730 | catII_from_Escherichia_coli_K-12 | 0/0 | 100.0 | 96.1 | X53796.1:186-828 | catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol. | phenicol |
| contig00230 | 2634 | 3509 | CTX-M-15 | 0/0 | 100.0 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig02077 | 445 | 927 | dfrA14 | 0/0 | 100.0 | 99.8 | EU780012:2162-2645 | dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli | diaminopyrimidine |
| contig00515 | 2666 | 3139 | dfrA15 | 0/0 | 100.0 | 100.0 | KF534911:39-513 | dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae | diaminopyrimidine |
| contig00120 | 6170 | 7363 | Enterobacter_cloacae_acrA | 0/0 | 100.0 | 94.0 | DQ679966:299-1493 | AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig01080 | 578 | 1408 | OXA-1 | 0/0 | 100.0 | 100.0 | JN420336.1:2230-1399 | OXA-1 is a beta-lactamase found in E. coli | cephalosporin, penam |
| contig01687 | 1 | 642 | QnrB1 | 0/0 | 99.5 | 100.0 | DQ351241.1:36-681 | QnrB1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae | fluoroquinolone |
| contig00231 | 4020 | 4371 | ramA | 0/0 | 93.9 | 90.9 | JQ727668:0-375 | RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. | carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan |
| contig00515 | 429 | 1268 | sul1 | 0/0 | 100.0 | 99.9 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00012 | 2816 | 3676 | TEM-150 | 0/0 | 100.0 | 99.9 | AM183304:208-1069 | TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae. | cephalosporin, monobactam, penam, penem |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00899 | 1696 | 2556 | (AGly)aac3-IIa | 0/0 | 100.0 | 99.8 | X51534:91-951 | (AGly)aac3-IIa | NA |
| contig00515 | 1773 | 2574 | (AGly)aadA1-pm | 0/0 | 96.5 | 99.9 | JQ690540:7968-8798 | (AGly)aadA1-pm | NA |
| contig01058 | 1408 | 2211 | (AGly)strA | 0/0 | 100.0 | 99.9 | AB366441:22458-23261 | (AGly)strA | NA |
| contig01058 | 572 | 1408 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00346 | 2791 | 3936 | (Bla)blaACT-16 | 0/0 | 100.0 | 99.1 | :NG_050702 | (Bla)blaACT-16 | NA |
| contig00047 | 3060 | 4205 | (Bla)blaACT-6 | 0/0 | 100.0 | 91.9 | FJ237366:41-1186 | (Bla)blaACT-6 | NA |
| contig00230 | 2634 | 3509 | (Bla)blaCTX-M-15 | 0/0 | 100.0 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig01080 | 578 | 1408 | (Bla)blaOXA-1 | 0/0 | 100.0 | 100.0 | JQ682867:1-831 | (Bla)blaOXA-1 | NA |
| contig00012 | 2816 | 3676 | (Bla)blaTEM-150 | 0/0 | 100.0 | 99.9 | AM183304:209-1069 | (Bla)blaTEM-150 | NA |
| contig01687 | 1 | 642 | (Flq)qnrB1 | 0/0 | 94.3 | 100.0 | DQ351241:1-681 | (Flq)qnrB1 | NA |
| contig01588 | 89 | 730 | (Phe)catA2 | 0/0 | 100.0 | 96.1 | X53796:187-903 | (Phe)catA2 | NA |
| contig00515 | 429 | 1268 | (Sul)sul1 | 0/0 | 100.0 | 99.9 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig02077 | 445 | 918 | (Tmt)dfrA14 | 0/0 | 100.0 | 100.0 | GU726917:72-545 | (Tmt)dfrA14 | NA |
| contig00515 | 2666 | 3139 | (Tmt)dfrA15b | 0/0 | 100.0 | 99.2 | AJ867237:177-650 | (Tmt)dfrA15b | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00899 | 1696 | 2556 | aac(3)-IIe | 0/0 | 100.0 | 99.8 | NG_047244.1 | aminoglycoside N-acetyltransferase AAC(3)-IIe | GENTAMICIN |
| contig01080 | 1539 | 2093 | aac(6’)-Ib-D181Y | 0/0 | 100.0 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00515 | 1773 | 2564 | aadA1 | 0/0 | 100.0 | 99.9 | NG_052266.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig01058 | 1408 | 2235 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig01058 | 572 | 1408 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00346 | 2791 | 3936 | blaACT-45 | 0/0 | 100.0 | 100.0 | NG_050708.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-45 | CEPHALOSPORIN |
| contig00047 | 3060 | 4205 | blaACT-63 | 0/0 | 100.0 | 99.4 | NG_061406.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-63 | CEPHALOSPORIN |
| contig00230 | 2634 | 3509 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig01080 | 578 | 1408 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig00012 | 2816 | 3676 | blaTEM-150 | 0/0 | 100.0 | 99.9 | NG_050194.1 | class A beta-lactamase TEM-150 | BETA-LACTAM |
| contig01588 | 89 | 730 | catA2 | 0/0 | 100.0 | 100.0 | NG_047596.1 | type A-2 chloramphenicol O-acetyltransferase CatII | CHLORAMPHENICOL |
| contig02077 | 445 | 918 | dfrA14 | 0/0 | 100.0 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00515 | 2666 | 3139 | dfrA15 | 0/0 | 100.0 | 100.0 | NG_047702.1 | trimethoprim-resistant dihydrofolate reductase DfrA15 | TRIMETHOPRIM |
| contig01687 | 1 | 642 | qnrB1 | 0/0 | 99.5 | 100.0 | NG_050469.1 | quinolone resistance pentapeptide repeat protein QnrB1 | QUINOLONE |
| contig00515 | 429 | 1268 | sul1 | 0/0 | 100.0 | 99.9 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00899 | 1696 | 2556 | aac(3)-IIe | 0/0 | 100.0 | 99.8 | NG_047244.1 | aminoglycoside N-acetyltransferase AAC(3)-IIe | GENTAMICIN |
| contig01080 | 1539 | 2093 | aac(6’)-Ib-D181Y | 0/0 | 100.0 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00515 | 1773 | 2564 | aadA1 | 0/0 | 100.0 | 99.9 | NG_052266.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig01058 | 1408 | 2235 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig01058 | 572 | 1408 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00346 | 2791 | 3936 | blaACT-45 | 0/0 | 100.0 | 100.0 | NG_050708.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-45 | CEPHALOSPORIN |
| contig00047 | 3060 | 4205 | blaACT-63 | 0/0 | 100.0 | 99.4 | NG_061406.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-63 | CEPHALOSPORIN |
| contig00230 | 2634 | 3509 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig01080 | 578 | 1408 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig00012 | 2816 | 3676 | blaTEM-150 | 0/0 | 100.0 | 99.9 | NG_050194.1 | class A beta-lactamase TEM-150 | BETA-LACTAM |
| contig01588 | 89 | 730 | catA2 | 0/0 | 100.0 | 100.0 | NG_047596.1 | type A-2 chloramphenicol O-acetyltransferase CatII | CHLORAMPHENICOL |
| contig02077 | 445 | 918 | dfrA14 | 0/0 | 100.0 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00515 | 2666 | 3139 | dfrA15 | 0/0 | 100.0 | 100.0 | NG_047702.1 | trimethoprim-resistant dihydrofolate reductase DfrA15 | TRIMETHOPRIM |
| contig01687 | 1 | 642 | qnrB1 | 0/0 | 99.5 | 100.0 | NG_050469.1 | quinolone resistance pentapeptide repeat protein QnrB1 | QUINOLONE |
| contig00515 | 429 | 1268 | sul1 | 0/0 | 100.0 | 99.9 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00082 | 1696 | 2556 | aac(3)-IIa_1 | 0/0 | 100.0 | 99.8 | X51534 | aac(3)-IIa | Gentamicin, Tobramycin |
| contig00084 | 1539 | 2138 | aac(6’)-Ib-cr_1 | 0/0 | 100.0 | 100.0 | DQ303918 | aac(6’)-Ib-cr | Ciprofloxacin |
| contig00092 | 126 | 1090 | ant(3’’)-Ia_1 | 3/7 | 99.3 | 99.1 | X02340 | ant(3’’)-Ia | Streptomycin |
| contig00067 | 3533 | 4336 | aph(3’’)-Ib_5 | 0/0 | 100.0 | 100.0 | AF321551 | aph(3’’)-Ib | Streptomycin |
| contig00067 | 2697 | 3533 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00006 | 95444 | 96589 | blaACT-7_1 | 0/0 | 100.0 | 99.6 | FJ237368 | blaACT-7 | |
| contig00076 | 2636 | 3511 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00084 | 578 | 1408 | blaOXA-1_1 | 0/0 | 100.0 | 100.0 | HQ170510 | blaOXA-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig00067 | 1116 | 1976 | blaTEM-1B_1 | 0/0 | 100.0 | 100.0 | AY458016 | blaTEM-1B | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig00087 | 350 | 1004 | catA1_1 | 0/0 | 99.2 | 99.8 | V00622 | catA1 | Chloramphenicol |
| contig00065 | 5401 | 5883 | dfrA14_5 | 0/0 | 100.0 | 99.6 | DQ388123 | dfrA14 | Trimethoprim |
| contig00058 | 9456 | 9881 | fosA_1 | 0/0 | 100.0 | 96.5 | M85195 | fosA | Fosfomycin |
| contig00066 | 4405 | 5049 | qnrB1_1 | 0/0 | 100.0 | 100.0 | DQ351241 | qnrB1 | Ciprofloxacin |
| contig00067 | 4397 | 5212 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00075 | 1429 | 2697 | tet(A)_6 | 1/22 | 97.8 | 93.2 | AF534183 | tet(A) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00082 | 1696 | 2556 | AAC(3)-IIe | 0/0 | 100.0 | 99.5 | EU022315.1:0-861 | AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig00084 | 1539 | 2138 | AAC(6’)-Ib-cr | 0/0 | 100.0 | 100.0 | DQ303918:0-600 | AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously | aminoglycoside, fluoroquinolone |
| contig00006 | 95444 | 96589 | ACT-17 | 0/0 | 100.0 | 99.6 | KF992026:753-1899 | ACT-17 is a beta-lactamase. From the Lahey list of ACT beta-lactamases. | carbapenem, cephalosporin, cephamycin, penam |
| contig00092 | 126 | 1090 | ANT(3’’)-IIa | 3/7 | 99.3 | 99.1 | X02340.1:222-1194 | ANT(3’’)-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms. | aminoglycoside |
| contig00067 | 3533 | 4336 | APH(3’’)-Ib | 0/0 | 100.0 | 99.8 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00067 | 2697 | 3533 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00087 | 350 | 1004 | catI | 0/0 | 99.2 | 99.8 | V00622:243-903 | catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii | phenicol |
| contig00076 | 2636 | 3511 | CTX-M-15 | 0/0 | 100.0 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig00065 | 5401 | 5883 | dfrA14 | 0/0 | 100.0 | 99.8 | EU780012:2162-2645 | dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli | diaminopyrimidine |
| contig00058 | 9456 | 9881 | FosA2 | 0/0 | 100.0 | 92.7 | EU487198:216-642 | An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. | fosfomycin |
| contig00084 | 578 | 1408 | OXA-1 | 0/0 | 100.0 | 100.0 | JN420336.1:2230-1399 | OXA-1 is a beta-lactamase found in E. coli | cephalosporin, penam |
| contig00066 | 4368 | 5049 | QnrB17 | 1/1 | 100.0 | 99.1 | AM919398:0-681 | QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii | fluoroquinolone |
| contig00067 | 4397 | 5212 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00067 | 1116 | 1976 | TEM-1 | 0/0 | 100.0 | 99.9 | AL513383:161910-162771 | TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. | cephalosporin, monobactam, penam, penem |
| contig00075 | 1429 | 2697 | tet(A) | 1/22 | 97.8 | 93.2 | AF534183.1:2970-4245 | TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00082 | 1696 | 2556 | (AGly)aac3-IIa | 0/0 | 100.0 | 99.8 | X51534:91-951 | (AGly)aac3-IIa | NA |
| contig00092 | 126 | 937 | (AGly)aadA1-pm | 0/0 | 97.7 | 99.9 | JQ690540:7968-8798 | (AGly)aadA1-pm | NA |
| contig00067 | 3533 | 4336 | (AGly)strA | 0/0 | 100.0 | 99.9 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00067 | 2697 | 3533 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00006 | 95444 | 96589 | (Bla)blaACT-7 | 0/0 | 100.0 | 99.6 | FJ237368:1-1146 | (Bla)blaACT-7 | NA |
| contig00076 | 2636 | 3511 | (Bla)blaCTX-M-15 | 0/0 | 100.0 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig00084 | 578 | 1408 | (Bla)blaOXA-1 | 0/0 | 100.0 | 100.0 | JQ682867:1-831 | (Bla)blaOXA-1 | NA |
| contig00067 | 1116 | 1976 | (Bla)blaTEM-105 | 0/0 | 100.0 | 99.9 | AF516720:215-1075 | (Bla)blaTEM-105 | NA |
| contig00058 | 9456 | 9881 | (Fcyn)FosA2 | 0/0 | 100.0 | 92.7 | EU487198:217-642 | (Fcyn)FosA2 | NA |
| contig00066 | 4368 | 5049 | (Flq)qnrB1 | 1/1 | 100.0 | 99.8 | DQ351241:1-681 | (Flq)qnrB1 | NA |
| contig00087 | 350 | 1004 | (Phe)catA1 | 0/0 | 99.2 | 99.8 | V00622:244-903 | (Phe)catA1 | NA |
| contig00067 | 4397 | 5212 | (Sul)sul2 | 0/0 | 100.0 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00075 | 1429 | 2725 | (Tet)tetA | 1/22 | 100.0 | 93.3 | JX424423:94438-95712 | (Tet)tetA | NA |
| contig00075 | 757 | 1398 | (Tet)tetR | 1/9 | 98.6 | 93.1 | HF545434:53576-54226 | (Tet)tetR | NA |
| contig00065 | 5401 | 5874 | (Tmt)dfrA14 | 0/0 | 100.0 | 100.0 | GU726917:72-545 | (Tmt)dfrA14 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00082 | 1696 | 2556 | aac(3)-IIe | 0/0 | 100.0 | 99.8 | NG_047244.1 | aminoglycoside N-acetyltransferase AAC(3)-IIe | GENTAMICIN |
| contig00084 | 1539 | 2093 | aac(6’)-Ib-D181Y | 0/0 | 100.0 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00092 | 126 | 917 | aadA1 | 0/0 | 100.0 | 100.0 | NG_052536.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig00067 | 3533 | 4360 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00067 | 2697 | 3533 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00006 | 95444 | 96589 | blaACT-40 | 0/0 | 100.0 | 100.0 | NG_050703.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-40 | CEPHALOSPORIN |
| contig00076 | 2636 | 3511 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00084 | 578 | 1408 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig00067 | 1116 | 1976 | blaTEM-1 | 0/0 | 100.0 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00087 | 350 | 1004 | catA1 | 0/0 | 99.2 | 99.8 | NG_047582.1 | type A-1 chloramphenicol O-acetyltransferase | CHLORAMPHENICOL |
| contig00065 | 5401 | 5874 | dfrA14 | 0/0 | 100.0 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00058 | 9456 | 9881 | fosA | 0/0 | 100.0 | 96.5 | NG_050405.1 | fosfomycin resistance glutathione transferase FosA | FOSFOMYCIN |
| contig00066 | 4405 | 5049 | qnrB1 | 0/0 | 100.0 | 100.0 | NG_050469.1 | quinolone resistance pentapeptide repeat protein QnrB1 | QUINOLONE |
| contig00067 | 4397 | 5212 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00075 | 1526 | 2725 | tet(A) | 0/0 | 100.0 | 100.0 | NG_048157.1 | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00082 | 1696 | 2556 | aac(3)-IIe | 0/0 | 100.0 | 99.8 | NG_047244.1 | aminoglycoside N-acetyltransferase AAC(3)-IIe | GENTAMICIN |
| contig00084 | 1539 | 2093 | aac(6’)-Ib-D181Y | 0/0 | 100.0 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00092 | 126 | 917 | aadA1 | 0/0 | 100.0 | 100.0 | NG_052536.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig00067 | 3533 | 4360 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00067 | 2697 | 3533 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00006 | 95444 | 96589 | blaACT-40 | 0/0 | 100.0 | 100.0 | NG_050703.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-40 | CEPHALOSPORIN |
| contig00076 | 2636 | 3511 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00084 | 578 | 1408 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig00067 | 1116 | 1976 | blaTEM-1 | 0/0 | 100.0 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00087 | 350 | 1004 | catA1 | 0/0 | 99.2 | 99.8 | NG_047582.1 | type A-1 chloramphenicol O-acetyltransferase | CHLORAMPHENICOL |
| contig00065 | 5401 | 5874 | dfrA14 | 0/0 | 100.0 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00058 | 9456 | 9881 | fosA | 0/0 | 100.0 | 96.5 | NG_050405.1 | fosfomycin resistance glutathione transferase FosA | FOSFOMYCIN |
| contig00066 | 4405 | 5049 | qnrB1 | 0/0 | 100.0 | 100.0 | NG_050469.1 | quinolone resistance pentapeptide repeat protein QnrB1 | QUINOLONE |
| contig00067 | 4397 | 5212 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00075 | 1526 | 2725 | tet(A) | 0/0 | 100.0 | 100.0 | NG_048157.1 | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE |
Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Gaps | Gaps in subject (genome) and query (antibiotic resistance gene) |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00032 | 16028 | 16623 | RepA_1_pKPC-CAV1321 | 0/0 | 100 | 100 | CP011611 | RepA_1_pKPC-CAV1321_CP011611 |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00553 | 1798 | 2440 | IncFIB(pB171)_1_pB171 | 0/0 | 100 | 91.5 | AB024946 | IncFIB(pB171)_1_pB171_AB024946 |
| contig00213 | 3438 | 3997 | IncFIB(pECLA)_1_pECLA | 0/0 | 100 | 100.0 | CP001919 | IncFIB(pECLA)_1_pECLA_CP001919 |
| contig00226 | 6578 | 7324 | IncFII(pECLA)_1_pECLA | 0/0 | 100 | 100.0 | CP001919 | IncFII(pECLA)_1_pECLA_CP001919 |
| contig00310 | 3749 | 3978 | IncFII(Yp)_1_Yersenia | 0/0 | 100 | 99.6 | CP000670 | IncFII(Yp)_1_Yersenia_CP000670 |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00042 | 7952 | 8698 | IncFII(pECLA)_1_pECLA | 0/0 | 100 | 97.3 | CP001919 | IncFII(pECLA)_1_pECLA_CP001919 |
| contig00041 | 28465 | 28791 | IncHI2_1 | 0/0 | 100 | 100.0 | BX664015 | IncHI2_1__BX664015 |
| contig00019 | 84375 | 85004 | IncHI2A_1 | 0/0 | 100 | 100.0 | BX664015 | IncHI2A_1__BX664015 |
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00001 | 339615 | 340109 | + | chuX | 100.0 | 82.2 | NP_756177 | (chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073] |
| contig00006 | 71670 | 72128 | - | csgB | 100.0 | 81.7 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00006 | 72890 | 73540 | + | csgD | 100.0 | 83.6 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00006 | 73545 | 73937 | + | csgE | 99.2 | 82.8 | NP_460112 | (csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00006 | 73963 | 74376 | + | csgF | 99.3 | 81.1 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00006 | 74402 | 75235 | + | csgG | 99.8 | 82.3 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00001 | 209564 | 210421 | - | entB | 100.0 | 80.7 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00001 | 210435 | 212045 | - | entE | 99.9 | 81.6 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00001 | 217796 | 218583 | + | fepC | 96.6 | 81.1 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00011 | 141012 | 141997 | + | fliG | 99.3 | 80.5 | YP_001006742 | (fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081] |
| contig00006 | 131252 | 132310 | + | ompA | 99.5 | 87.3 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00165 | 9121 | 9235 | - | astA | 98.3 | 91.3 | BAA94855 | (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042] |
| contig00024 | 1898 | 2731 | - | csgG | 100.0 | 81.7 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00055 | 10436 | 10972 | - | lpfA | 100.0 | 89.2 | NP_462541 | (lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00055 | 9652 | 10350 | - | lpfB | 100.0 | 89.1 | NP_462540 | (lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00055 | 7101 | 9629 | - | lpfC | 100.0 | 90.1 | NP_462539 | (lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00055 | 5474 | 6001 | - | lpfE | 100.0 | 83.3 | NP_462537 | (lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00133 | 42 | 941 | + | ompA | 86.2 | 84.8 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00020 | 83752 | 84581 | + | csgG | 99.4 | 80.8 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00024 | 36938 | 38100 | - | iroB | 99.9 | 89.8 | NP_753168 | (iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073] |
| contig00024 | 33151 | 36878 | - | iroC | 99.6 | 89.0 | NP_753167 | (iroC) ATP binding cassette transporter [Salmochelin (IA013)] [Escherichia coli CFT073] |
| contig00024 | 31806 | 33035 | - | iroD | 100.0 | 87.8 | NP_753166 | (iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073] |
| contig00024 | 30766 | 31722 | - | iroE | 100.0 | 86.9 | NP_753165 | (iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073] |
| contig00024 | 28547 | 30721 | + | iroN | 99.9 | 91.1 | NP_753164 | (iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073] |
| contig00032 | 22908 | 23950 | - | ompA | 99.0 | 84.7 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| Symbol | Meaning |
|---|---|
| ~ | novel full length allele similar to match |
| ? | partial match to known allele |
| - | allele missing |
| Scheme | ST | 1 | 2 | 3 | 4 | 5 | 6 | 7 | |
|---|---|---|---|---|---|---|---|---|---|
| ID084I | cfreundii | 263 | aspC(16) | clpX(30) | fadD(33) | mdh(28) | arcA(5) | dnaG(28) | lysP(74) |
| ORTHO013EII | ecloacae | - | dnaA(52) | fusA(106) | gyrB(20) | leuS(44,237) | pyrG(45) | rplB(12) | rpoB(148) |
| ORTHO039E | ecloacae | 1015 | dnaA(4) | fusA(4) | gyrB(68) | leuS(6) | pyrG(39) | rplB(4) | rpoB(25) |
| Genes | Description | Number |
|---|---|---|
| Core genes | (99% <= strains <= 100%) | 343 |
| Soft core genes | (95% <= strains < 99%) | 0 |
| Shell genes | (15% <= strains < 95%) | 14102 |
| Cloud genes | (0% <= strains < 15%) | 0 |
| Total genes | (0% <= strains <= 100%) | 14445 |
| Field | Description |
|---|---|
| Region | Numeric code given to insertion sequence (IS) |
| Orientation | The orientation of IS position: Either forward (F) or reverse (F) |
| X-cordinates | The left coordinate of the position |
| Y-coordinates | The right coordinate of the position |
| Gap | The distance between the x and y coordinates |
| CallType | Describes whether a position hit is novel (not in reference) or known (in the reference) |
| LeftGene | Locus tag ID of the gene closest to the left side of the IS position |
| LeftGeneDescription | Description of the gene feature from the left side of the IS position. By default this is the product position |
| RightGene | Locus tag ID of the gene closest to the right side of the IS position |
| RightGeneDescription | Description of the gene feature from the right side of the IS position. By default this is the product position |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | R | -1 | 2023638 | 2023639 | novel | CfB38_4905 | 50S ribosomal protein L34 | CfB38_1939 | IS1 insA protein |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | R | -1 | 847919 | 847920 | novel | CfB38_4905 | 50S ribosomal protein L34 | CfB38_0804 | N-glycosyltransferase |
If you have used rMAP, please cite:
Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583
The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite: